Encryption will never help for this on its own, as every user who has to run it also needs to be able to decrypt it.

If you need non-admin users to run a backup script, you should use something like sudo to give them the rights to run that script but not the rights to read the passwords (i.e. make sure the permissions are set such that the user can't read them).

Do normal users need to be able to run these scripts? Presumably you could have a backup user and set the permissions on the script to 700. If you really needed to let other people to run the script you could use sudo. You have very little chance of hiding the passwords from the root user.